During 2020, the Covid-19 pandemic unleashed a socioeconomic crisis in most countries, as well as strict restrictions on mobility and social distancing were implemented. The pandemic brought a severe socioeconomic shock -decreasing economic activity- and forced policy responses that affected the education sector -notably school closures-. There is scarce evidence on the implications of the pandemic and its socioeconomic consequences on learning inequality, particularly in the Latin-American context. The aim of this paper is to measure the change in learning inequality during the years of the pandemic (2020–2021) in Colombia. To measure learning inequality, we use the results of a standardize exam taken by all upper secondary education graduates in the country. To capture inequality, we use secondary-level students’ characteristics, their households, and schools’ characteristics. Our econometric results suggest an increase in learning inequality between 48% and 372% depending on the dimension studied, except for gender where learning inequality decreased. Moreover, through dynamic specifications, we determine that for all the analyzed dimensions the 2020–2021 period represents a change in the trend of learning inequality as in the periods prior to the pandemic inequality gaps decreased or, at least, remained constant. We conclude with concrete and immediate policy recommendations to target the learning processes of vulnerable students and bridge learning gaps.